Re: extra bonds

From: Josh Vermaas (
Date: Thu Jul 02 2015 - 09:48:22 CDT

Hi Lara,

I think you would benefit from reading up a bit more on the CHARMM force
field, and what the individual terms mean. The NAMD tutorial has some
more detailed explanations
but basically you will want to use the first specification, since you
want to keep the sugar at a specific pucker, which can be done with
harmonically constrained dihedral angles going around the ring (ie. the
potential you want to add is like k*(phi-ref)^2). The second
specification is if you want to add another k*(1+cos(n*phi-ref))
potential term. Impropers are "fake" dihedrals that do not describe
rotation about a bond, and are usually used to keep a planar part of the
molecule planar.

The size of k depends on how big of a tolerance you have for deviations
from the ideal geometry. kT at room temperature is ~0.6 kcal/mol. How
much deviation are you willing to tolerate when you run your simulation?

-Josh Vermaas

On 07/02/2015 09:20 AM, Lara rajam wrote:
> Dear NAMD users !
> I would like to fix the sugar puckering during the simulation.
> how it should be done in NAMD , do i need to use the dihedral or the
> improper flag in the extra bonds.
> I have read through and got information like
> * dihedral <atom> <atom> <atom> <atom> <k> <ref>
> * dihedral <atom> <atom> <atom> <atom> <k> <n> <ref>
> * improper <atom> <atom> <atom> <atom> <k> <ref>
> * improper <atom> <atom> <atom> <atom> <k> <n> <ref>
> my question is K refers to the spring constant , what should be the
> value given to it and what does the other flag n refer to .
> if more information is given it will improve my understanding !
> thank you !

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